4.9 readOverlap

Estimating distribution of overlap of paired reads in BAM file

readOverlap assesses how many pairs in Paired-end sequenced reads have a given overlap.

4.9.1 Input

Required inputs :

--bam Input_bam_file.bam

Input BAM file.

Optional inputs :

• None

Specific Parameters :

• None

Engine parameters that are common to all tasks can be found here.

4.9.2 Output

*_overlapStats.txt	A text file with infromation about reads overlap.
*_filterSummary.txt	A text file with filter summary.

4.9.3 Usage Example

#! /bin/bash

. $(dirname $0)/find_atlas
. $(dirname $0)/simulate --seqType single \
    --fixedSeed 200 --out single --logFile single_simulate.out 

. $(dirname $0)/simulate --seqType paired \
    --fixedSeed 201 --out paired --logFile paired_simulate.out 

for f in *.bam; do
    out=${f%.bam}
    $atlas --task readOverlap --bam $f \
           --fixedSeed 202 --out $out --logFile $out.out 2> $out.eout
done